Render this script with > sbatch ~/spinal_cord_paper/scripts/Seurat_Gg_NT_int_array.sh

load the data

the following workflow is based on: - [https://github.com/satijalab/seurat/issues/1500] Cell cycle regression - [https://github.com/satijalab/seurat/issues/1836] General workflow - [https://github.com/satijalab/seurat/issues/2590] Integrate all features (although used in the integration script)

library(Seurat)
library(dplyr)
library(Rtsne)
library(RColorBrewer)
library(tidyr)
library(ggplot2)
library(gridExtra)
library(patchwork)
library(cowplot)
library(ggdendro)

gnames <- modplots::gnames
# load the integrated seurat
my.int <- readRDS(file = "~/spinal_cord_paper/data/Gg_lumb_integrated_250723.rds")

my.int@project.name <- "Gg_lumb_int"

my.int

Date: 25.07.23

inspect

We order the plot by nCount_RNA to prevent overplotting of the last sample (default order is the group.by ident).

# have a look at the PC and the previously calculated UMAP
PCAPlot(
  my.int,
  group.by = "orig.ident",
  order = "nCount_RNA"
  )


DimPlot(
  my.int,
  reduction = "umap",
  group.by = "orig.ident",
  order = "nCount_RNA"
  )

cell cycle scoring

Now we can score the cell cycle stage, using Seurats function. For this wee need the ortholog of the distributed cell stage marker lists.

We do the CC.difference calculation at this stage - and not prior to integration - based on the suggestion from: [https://github.com/satijalab/seurat/issues/1500]

We add the scores of stages S and G2M, as well as the difference between them to the metadata with the names: S, G2M, CC.Difference

knitr::opts_chunk$set(
  comment = '', fig.width = 10, fig.height = 7
)

PCA plot of non-regressed data

# Load the orhtology table
ortho_gg_mm_v102 <- readRDS("~/spinal_cord_paper/data/ortho_gg_mm_v102.rds") 

colnames(ortho_gg_mm_v102) <- c(
  "GG_gene_ID",
  "GG_gene_Name",
  "MM_gene_ID",
  "MM_gene_Name",
  "ortho_conf",
  "homolog_type"
)

# A list of cell cycle markers, from Tirosh et al, 2015, is loaded with Seurat.  We can
# segregate this list into markers of G2/M phase and markers of S phase
s.genes <- ortho_gg_mm_v102 %>%
  dplyr::mutate(MM_gene_Name = toupper(MM_gene_Name)) %>%
  dplyr::filter(MM_gene_Name %in% cc.genes$s.genes) %>%
  dplyr::arrange(match(MM_gene_Name, cc.genes$s.genes)) %>%
  dplyr::pull(GG_gene_ID)

g2m.genes <- ortho_gg_mm_v102 %>%
  dplyr::mutate(MM_gene_Name = toupper(MM_gene_Name)) %>%
  dplyr::filter(MM_gene_Name %in% cc.genes$g2m.genes) %>%
  dplyr::arrange(match(MM_gene_Name, cc.genes$g2m.genes)) %>%
  dplyr::pull(GG_gene_ID) 

t0 <- Sys.time()
my.int <- CellCycleScoring(
  my.int,
  s.features = s.genes,
  g2m.features = g2m.genes,
  set.ident = TRUE
  )
Warning: The following features are not present in the object: ENSGALG00000033063, ENSGALG00000041973, ENSGALG00000000734, ENSGALG00000013626, ENSGALG00000040794, ENSGALG00000010842, ENSGALG00000008962, ENSGALG00000010748, ENSGALG00000007649, ENSGALG00000043799, ENSGALG00000008256, ENSGALG00000015611, ENSGALG00000010957, ENSGALG00000016042, ENSGALG00000005279, not searching for symbol synonyms
Warning: The following features are not present in the object: ENSGALG00000038817, ENSGALG00000039891, ENSGALG00000001817, ENSGALG00000036856, ENSGALG00000037735, not searching for symbol synonyms
paste0("Seurats CC scoring took ", Sys.time() - t0, " seconds to run.")
[1] "Seurats CC scoring took 1.42294955253601 seconds to run."
my.int$CC.Difference.seurat <- my.int$S.Score - my.int$G2M.Score
# view cell cycle scores and phase assignments
head(my.int[[]])

rm(t0, s.genes, g2m.genes)

rescale integrated assay

We rescale the data to regress out the CC.difference

all_genes <- rownames(my.int)

my.int <- ScaleData(
  my.int,
  features = all_genes,
  vars.to.regress = "CC.Difference.seurat"
)
Regressing out CC.Difference.seurat

  |                                                                                                                                                
  |                                                                                                                                          |   0%
  |                                                                                                                                                
  |=                                                                                                                                         |   0%
  |                                                                                                                                                
  |=                                                                                                                                         |   1%
  |                                                                                                                                                
  |==                                                                                                                                        |   1%
  |                                                                                                                                                
  |==                                                                                                                                        |   2%
  |                                                                                                                                                
  |===                                                                                                                                       |   2%
  |                                                                                                                                                
  |===                                                                                                                                       |   3%
  |                                                                                                                                                
  |====                                                                                                                                      |   3%
  |                                                                                                                                                
  |=====                                                                                                                                     |   3%
  |                                                                                                                                                
  |=====                                                                                                                                     |   4%
  |                                                                                                                                                
  |======                                                                                                                                    |   4%
  |                                                                                                                                                
  |======                                                                                                                                    |   5%
  |                                                                                                                                                
  |=======                                                                                                                                   |   5%
  |                                                                                                                                                
  |========                                                                                                                                  |   5%
  |                                                                                                                                                
  |========                                                                                                                                  |   6%
  |                                                                                                                                                
  |=========                                                                                                                                 |   6%
  |                                                                                                                                                
  |=========                                                                                                                                 |   7%
  |                                                                                                                                                
  |==========                                                                                                                                |   7%
  |                                                                                                                                                
  |==========                                                                                                                                |   8%
  |                                                                                                                                                
  |===========                                                                                                                               |   8%
  |                                                                                                                                                
  |============                                                                                                                              |   8%
  |                                                                                                                                                
  |============                                                                                                                              |   9%
  |                                                                                                                                                
  |=============                                                                                                                             |   9%
  |                                                                                                                                                
  |=============                                                                                                                             |  10%
  |                                                                                                                                                
  |==============                                                                                                                            |  10%
  |                                                                                                                                                
  |===============                                                                                                                           |  11%
  |                                                                                                                                                
  |================                                                                                                                          |  11%
  |                                                                                                                                                
  |================                                                                                                                          |  12%
  |                                                                                                                                                
  |=================                                                                                                                         |  12%
  |                                                                                                                                                
  |=================                                                                                                                         |  13%
  |                                                                                                                                                
  |==================                                                                                                                        |  13%
  |                                                                                                                                                
  |===================                                                                                                                       |  13%
  |                                                                                                                                                
  |===================                                                                                                                       |  14%
  |                                                                                                                                                
  |====================                                                                                                                      |  14%
  |                                                                                                                                                
  |====================                                                                                                                      |  15%
  |                                                                                                                                                
  |=====================                                                                                                                     |  15%
  |                                                                                                                                                
  |=====================                                                                                                                     |  16%
  |                                                                                                                                                
  |======================                                                                                                                    |  16%
  |                                                                                                                                                
  |=======================                                                                                                                   |  16%
  |                                                                                                                                                
  |=======================                                                                                                                   |  17%
  |                                                                                                                                                
  |========================                                                                                                                  |  17%
  |                                                                                                                                                
  |========================                                                                                                                  |  18%
  |                                                                                                                                                
  |=========================                                                                                                                 |  18%
  |                                                                                                                                                
  |==========================                                                                                                                |  18%
  |                                                                                                                                                
  |==========================                                                                                                                |  19%
  |                                                                                                                                                
  |===========================                                                                                                               |  19%
  |                                                                                                                                                
  |===========================                                                                                                               |  20%
  |                                                                                                                                                
  |============================                                                                                                              |  20%
  |                                                                                                                                                
  |============================                                                                                                              |  21%
  |                                                                                                                                                
  |=============================                                                                                                             |  21%
  |                                                                                                                                                
  |==============================                                                                                                            |  21%
  |                                                                                                                                                
  |==============================                                                                                                            |  22%
  |                                                                                                                                                
  |===============================                                                                                                           |  22%
  |                                                                                                                                                
  |===============================                                                                                                           |  23%
  |                                                                                                                                                
  |================================                                                                                                          |  23%
  |                                                                                                                                                
  |================================                                                                                                          |  24%
  |                                                                                                                                                
  |=================================                                                                                                         |  24%
  |                                                                                                                                                
  |==================================                                                                                                        |  24%
  |                                                                                                                                                
  |==================================                                                                                                        |  25%
  |                                                                                                                                                
  |===================================                                                                                                       |  25%
  |                                                                                                                                                
  |===================================                                                                                                       |  26%
  |                                                                                                                                                
  |====================================                                                                                                      |  26%
  |                                                                                                                                                
  |=====================================                                                                                                     |  26%
  |                                                                                                                                                
  |=====================================                                                                                                     |  27%
  |                                                                                                                                                
  |======================================                                                                                                    |  27%
  |                                                                                                                                                
  |======================================                                                                                                    |  28%
  |                                                                                                                                                
  |=======================================                                                                                                   |  28%
  |                                                                                                                                                
  |=======================================                                                                                                   |  29%
  |                                                                                                                                                
  |========================================                                                                                                  |  29%
  |                                                                                                                                                
  |=========================================                                                                                                 |  29%
  |                                                                                                                                                
  |=========================================                                                                                                 |  30%
  |                                                                                                                                                
  |==========================================                                                                                                |  30%
  |                                                                                                                                                
  |==========================================                                                                                                |  31%
  |                                                                                                                                                
  |===========================================                                                                                               |  31%
  |                                                                                                                                                
  |===========================================                                                                                               |  32%
  |                                                                                                                                                
  |============================================                                                                                              |  32%
  |                                                                                                                                                
  |=============================================                                                                                             |  32%
  |                                                                                                                                                
  |=============================================                                                                                             |  33%
  |                                                                                                                                                
  |==============================================                                                                                            |  33%
  |                                                                                                                                                
  |==============================================                                                                                            |  34%
  |                                                                                                                                                
  |===============================================                                                                                           |  34%
  |                                                                                                                                                
  |================================================                                                                                          |  34%
  |                                                                                                                                                
  |================================================                                                                                          |  35%
  |                                                                                                                                                
  |=================================================                                                                                         |  35%
  |                                                                                                                                                
  |=================================================                                                                                         |  36%
  |                                                                                                                                                
  |==================================================                                                                                        |  36%
  |                                                                                                                                                
  |==================================================                                                                                        |  37%
  |                                                                                                                                                
  |===================================================                                                                                       |  37%
  |                                                                                                                                                
  |====================================================                                                                                      |  37%
  |                                                                                                                                                
  |====================================================                                                                                      |  38%
  |                                                                                                                                                
  |=====================================================                                                                                     |  38%
  |                                                                                                                                                
  |=====================================================                                                                                     |  39%
  |                                                                                                                                                
  |======================================================                                                                                    |  39%
  |                                                                                                                                                
  |=======================================================                                                                                   |  40%
  |                                                                                                                                                
  |========================================================                                                                                  |  40%
  |                                                                                                                                                
  |========================================================                                                                                  |  41%
  |                                                                                                                                                
  |=========================================================                                                                                 |  41%
  |                                                                                                                                                
  |=========================================================                                                                                 |  42%
  |                                                                                                                                                
  |==========================================================                                                                                |  42%
  |                                                                                                                                                
  |===========================================================                                                                               |  42%
  |                                                                                                                                                
  |===========================================================                                                                               |  43%
  |                                                                                                                                                
  |============================================================                                                                              |  43%
  |                                                                                                                                                
  |============================================================                                                                              |  44%
  |                                                                                                                                                
  |=============================================================                                                                             |  44%
  |                                                                                                                                                
  |=============================================================                                                                             |  45%
  |                                                                                                                                                
  |==============================================================                                                                            |  45%
  |                                                                                                                                                
  |===============================================================                                                                           |  45%
  |                                                                                                                                                
  |===============================================================                                                                           |  46%
  |                                                                                                                                                
  |================================================================                                                                          |  46%
  |                                                                                                                                                
  |================================================================                                                                          |  47%
  |                                                                                                                                                
  |=================================================================                                                                         |  47%
  |                                                                                                                                                
  |==================================================================                                                                        |  47%
  |                                                                                                                                                
  |==================================================================                                                                        |  48%
  |                                                                                                                                                
  |===================================================================                                                                       |  48%
  |                                                                                                                                                
  |===================================================================                                                                       |  49%
  |                                                                                                                                                
  |====================================================================                                                                      |  49%
  |                                                                                                                                                
  |====================================================================                                                                      |  50%
  |                                                                                                                                                
  |=====================================================================                                                                     |  50%
  |                                                                                                                                                
  |======================================================================                                                                    |  50%
  |                                                                                                                                                
  |======================================================================                                                                    |  51%
  |                                                                                                                                                
  |=======================================================================                                                                   |  51%
  |                                                                                                                                                
  |=======================================================================                                                                   |  52%
  |                                                                                                                                                
  |========================================================================                                                                  |  52%
  |                                                                                                                                                
  |========================================================================                                                                  |  53%
  |                                                                                                                                                
  |=========================================================================                                                                 |  53%
  |                                                                                                                                                
  |==========================================================================                                                                |  53%
  |                                                                                                                                                
  |==========================================================================                                                                |  54%
  |                                                                                                                                                
  |===========================================================================                                                               |  54%
  |                                                                                                                                                
  |===========================================================================                                                               |  55%
  |                                                                                                                                                
  |============================================================================                                                              |  55%
  |                                                                                                                                                
  |=============================================================================                                                             |  55%
  |                                                                                                                                                
  |=============================================================================                                                             |  56%
  |                                                                                                                                                
  |==============================================================================                                                            |  56%
  |                                                                                                                                                
  |==============================================================================                                                            |  57%
  |                                                                                                                                                
  |===============================================================================                                                           |  57%
  |                                                                                                                                                
  |===============================================================================                                                           |  58%
  |                                                                                                                                                
  |================================================================================                                                          |  58%
  |                                                                                                                                                
  |=================================================================================                                                         |  58%
  |                                                                                                                                                
  |=================================================================================                                                         |  59%
  |                                                                                                                                                
  |==================================================================================                                                        |  59%
  |                                                                                                                                                
  |==================================================================================                                                        |  60%
  |                                                                                                                                                
  |===================================================================================                                                       |  60%
  |                                                                                                                                                
  |====================================================================================                                                      |  61%
  |                                                                                                                                                
  |=====================================================================================                                                     |  61%
  |                                                                                                                                                
  |=====================================================================================                                                     |  62%
  |                                                                                                                                                
  |======================================================================================                                                    |  62%
  |                                                                                                                                                
  |======================================================================================                                                    |  63%
  |                                                                                                                                                
  |=======================================================================================                                                   |  63%
  |                                                                                                                                                
  |========================================================================================                                                  |  63%
  |                                                                                                                                                
  |========================================================================================                                                  |  64%
  |                                                                                                                                                
  |=========================================================================================                                                 |  64%
  |                                                                                                                                                
  |=========================================================================================                                                 |  65%
  |                                                                                                                                                
  |==========================================================================================                                                |  65%
  |                                                                                                                                                
  |==========================================================================================                                                |  66%
  |                                                                                                                                                
  |===========================================================================================                                               |  66%
  |                                                                                                                                                
  |============================================================================================                                              |  66%
  |                                                                                                                                                
  |============================================================================================                                              |  67%
  |                                                                                                                                                
  |=============================================================================================                                             |  67%
  |                                                                                                                                                
  |=============================================================================================                                             |  68%
  |                                                                                                                                                
  |==============================================================================================                                            |  68%
  |                                                                                                                                                
  |===============================================================================================                                           |  68%
  |                                                                                                                                                
  |===============================================================================================                                           |  69%
  |                                                                                                                                                
  |================================================================================================                                          |  69%
  |                                                                                                                                                
  |================================================================================================                                          |  70%
  |                                                                                                                                                
  |=================================================================================================                                         |  70%
  |                                                                                                                                                
  |=================================================================================================                                         |  71%
  |                                                                                                                                                
  |==================================================================================================                                        |  71%
  |                                                                                                                                                
  |===================================================================================================                                       |  71%
  |                                                                                                                                                
  |===================================================================================================                                       |  72%
  |                                                                                                                                                
  |====================================================================================================                                      |  72%
  |                                                                                                                                                
  |====================================================================================================                                      |  73%
  |                                                                                                                                                
  |=====================================================================================================                                     |  73%
  |                                                                                                                                                
  |=====================================================================================================                                     |  74%
  |                                                                                                                                                
  |======================================================================================================                                    |  74%
  |                                                                                                                                                
  |=======================================================================================================                                   |  74%
  |                                                                                                                                                
  |=======================================================================================================                                   |  75%
  |                                                                                                                                                
  |========================================================================================================                                  |  75%
  |                                                                                                                                                
  |========================================================================================================                                  |  76%
  |                                                                                                                                                
  |=========================================================================================================                                 |  76%
  |                                                                                                                                                
  |==========================================================================================================                                |  76%
  |                                                                                                                                                
  |==========================================================================================================                                |  77%
  |                                                                                                                                                
  |===========================================================================================================                               |  77%
  |                                                                                                                                                
  |===========================================================================================================                               |  78%
  |                                                                                                                                                
  |============================================================================================================                              |  78%
  |                                                                                                                                                
  |============================================================================================================                              |  79%
  |                                                                                                                                                
  |=============================================================================================================                             |  79%
  |                                                                                                                                                
  |==============================================================================================================                            |  79%
  |                                                                                                                                                
  |==============================================================================================================                            |  80%
  |                                                                                                                                                
  |===============================================================================================================                           |  80%
  |                                                                                                                                                
  |===============================================================================================================                           |  81%
  |                                                                                                                                                
  |================================================================================================================                          |  81%
  |                                                                                                                                                
  |================================================================================================================                          |  82%
  |                                                                                                                                                
  |=================================================================================================================                         |  82%
  |                                                                                                                                                
  |==================================================================================================================                        |  82%
  |                                                                                                                                                
  |==================================================================================================================                        |  83%
  |                                                                                                                                                
  |===================================================================================================================                       |  83%
  |                                                                                                                                                
  |===================================================================================================================                       |  84%
  |                                                                                                                                                
  |====================================================================================================================                      |  84%
  |                                                                                                                                                
  |=====================================================================================================================                     |  84%
  |                                                                                                                                                
  |=====================================================================================================================                     |  85%
  |                                                                                                                                                
  |======================================================================================================================                    |  85%
  |                                                                                                                                                
  |======================================================================================================================                    |  86%
  |                                                                                                                                                
  |=======================================================================================================================                   |  86%
  |                                                                                                                                                
  |=======================================================================================================================                   |  87%
  |                                                                                                                                                
  |========================================================================================================================                  |  87%
  |                                                                                                                                                
  |=========================================================================================================================                 |  87%
  |                                                                                                                                                
  |=========================================================================================================================                 |  88%
  |                                                                                                                                                
  |==========================================================================================================================                |  88%
  |                                                                                                                                                
  |==========================================================================================================================                |  89%
  |                                                                                                                                                
  |===========================================================================================================================               |  89%
  |                                                                                                                                                
  |============================================================================================================================              |  90%
  |                                                                                                                                                
  |=============================================================================================================================             |  90%
  |                                                                                                                                                
  |=============================================================================================================================             |  91%
  |                                                                                                                                                
  |==============================================================================================================================            |  91%
  |                                                                                                                                                
  |==============================================================================================================================            |  92%
  |                                                                                                                                                
  |===============================================================================================================================           |  92%
  |                                                                                                                                                
  |================================================================================================================================          |  92%
  |                                                                                                                                                
  |================================================================================================================================          |  93%
  |                                                                                                                                                
  |=================================================================================================================================         |  93%
  |                                                                                                                                                
  |=================================================================================================================================         |  94%
  |                                                                                                                                                
  |==================================================================================================================================        |  94%
  |                                                                                                                                                
  |==================================================================================================================================        |  95%
  |                                                                                                                                                
  |===================================================================================================================================       |  95%
  |                                                                                                                                                
  |====================================================================================================================================      |  95%
  |                                                                                                                                                
  |====================================================================================================================================      |  96%
  |                                                                                                                                                
  |=====================================================================================================================================     |  96%
  |                                                                                                                                                
  |=====================================================================================================================================     |  97%
  |                                                                                                                                                
  |======================================================================================================================================    |  97%
  |                                                                                                                                                
  |=======================================================================================================================================   |  97%
  |                                                                                                                                                
  |=======================================================================================================================================   |  98%
  |                                                                                                                                                
  |========================================================================================================================================  |  98%
  |                                                                                                                                                
  |========================================================================================================================================  |  99%
  |                                                                                                                                                
  |========================================================================================================================================= |  99%
  |                                                                                                                                                
  |========================================================================================================================================= | 100%
  |                                                                                                                                                
  |==========================================================================================================================================| 100%
Centering and scaling data matrix

  |                                                                                                                                                
  |                                                                                                                                          |   0%
  |                                                                                                                                                
  |==============================================                                                                                            |  33%
  |                                                                                                                                                
  |============================================================================================                                              |  67%
  |                                                                                                                                                
  |==========================================================================================================================================| 100%

PCA

PCAPlot(my.int, group.by = "Phase")

Dim Reduction

We will run the tSNE. Using the FFT-accelerated Interpolation-based t-SNE (FIt-SNE). We run two, a normal tSNE, and an exaggerated tSNE, where clusters are tighter togheter. This is located under the xtsne name.


# Get the tSNE function
source("~/Software/FIt-SNE-master/fast_tsne.R")
my.tsne = fftRtsne(my.int@reductions$pca@cell.embeddings[,my.dimensions],
                   max_iter = 1500,
                   learning_rate =  round(dim(my.int)[2]/12),
                   initialization =(my.int@reductions$pca@cell.embeddings[,1:2]/my.int@reductions$pca@stdev[1])*0.0001,
                   perplexity_list = c(25, round(dim(my.int)[2]/100)),
                   fast_tsne_path="~/Software/FIt-SNE-master/bin/fast_tsne")
colnames(my.tsne) = c("tsne_1", "tsne_2")
rownames(my.tsne) = colnames(my.int)

my.int[["tsne"]] = CreateDimReducObject(embeddings = my.tsne, key = "tsne_", assay = DefaultAssay(my.int), global = T)

Clustering

Here we perform the Louvain-jaccard clustering implemented in Seurat. We can see the tree of clusters, to see how the clusters relate in the PCA space.
We also use the tree, to check if any of the terminal pairs of sisters should be merged. This is determined based on a minimum of 20 DEs between the clusters.


# Find first the nearest neighbors
my.int <- FindNeighbors(object = my.int, dims=my.dimensions, verbose = F)

# Then the actual clusters
my.int <- FindClusters(object = my.int, resolution = 1, verbose = F, random.seed = 42)

# Check the tree of clusters, to see what's the relationship between them
my.int <- BuildClusterTree(my.int, dims = my.dimensions, verbose = F)
plot(Tool(object = my.int, slot = 'BuildClusterTree'))


# We are gonna check for DEs using the non integrated data. We are only gonna test genes that have variability, so we calculate variable genes
my.int <- FindVariableFeatures(my.int, assay = "RNA")
# Only the genes with variability > median
my.HVF <- HVFInfo(my.int, assay = "RNA")
my.HVF <- rownames(my.HVF)[which(my.HVF[,3] > (median(my.HVF[,3])))]
# We check for pairs of clusters, how mayn DEs they have. If less than n, we merge them
keep.check <- T
while (keep.check == T) {
  
  keep.check <- F
  # Check the tree of clusters, to see what's the relationship between them
  my.int <- BuildClusterTree(my.int, dims = my.dimensions, verbose = F)
  # Check only the terminal sisters
  to.check = ips::terminalSisters(my.int@tools$BuildClusterTree)
  for (i in to.check) {
    # DE between the sisters
    my.DE <- FindMarkers(my.int, i[1], i[2], test.use = "MAST", latent.vars = c("CC.Difference.seurat"),
                         min.pct = 0.25, verbose = T, assay = "RNA", features = my.HVF,) %>%
      dplyr::filter(abs(avg_log2FC) > 0.5) %>%
      dplyr::filter(p_val_adj < 0.05)
    
    # If less than 5, merge, and repeat
    if (dim(my.DE)[1] < 5) {
      cat(paste0(dim(my.DE)[1], " genes differentially expressed between clusters ",i[1]," and ",i[2]," merging \n"))
      my.int <- SetIdent(my.int, cells = WhichCells(my.int, idents = i[2]), value = i[1])
      keep.check <- T
    }
    print(i)
  }
}
rm(to.check, my.HVF, my.DE)

# renumber starting from 1
my.ID <- factor(
  Idents(my.int),
  levels= levels(Idents(my.int))[base::order(as.numeric(levels(Idents(my.int))))])
levels(my.ID) <- seq(length(levels(my.ID)))
Idents(my.int) <- my.ID
my.int[["seurat_clusters"]] <- my.ID

# Check again the clusters
dim1 <- DimPlot(my.int, reduction = "tsne", cols = rainbow(length(levels(my.ID))), label = T, label.size = 5, pt.size = 1)
dim1

Plot the tree again

# tree based on PCA dims
my.int <- BuildClusterTree(my.int, dims = my.dimensions, verbose = F)
plot(Tool(object = my.int, slot = 'BuildClusterTree'))

Now that we have the final reductions, we’ll choose one and we look at the statistics of the cells.

# Run the actual PCA (by default uses var.features of assay)
my.int <- RunPCA(my.int, verbose = F)

PCAPlot(my.int, group.by = "Phase")


# Which dimensions will we choose?
hist(my.int@reductions$pca@stdev^2, breaks = 500)


my.dimensions=1:20

# set and get dim.reduct embeddings
my.reduc <- "tsne"
emb <- data.frame(Embeddings(my.int, my.reduc))
colnames(emb) <- c("reduc_1", "reduc_2")

meta <- my.int[[]] %>%
  tibble::rownames_to_column("cell_ID")


my.plots = list()

my.plots[[1]] = ggplot(emb[meta[order(meta$nCount_RNA),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$nCount_RNA)), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="UMI count", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[2]] = ggplot(emb[meta[order(meta$nFeature_RNA),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$nFeature_RNA)), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="gene count", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[3]] = ggplot(emb[meta[order(meta$nCount_SCT),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$nCount_RNA)), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="UMI count (SCT)", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[4]] = ggplot(emb[meta[order(meta$nFeature_SCT),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$nFeature_RNA)), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="gene count (SCT)", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[5]] = ggplot(emb[meta[order(meta$percent.mt),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=(sort(meta$percent.mt))), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="log1p MT percent", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[6]] = ggplot(emb[meta[order(meta$CC.Difference.seurat),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$CC.Difference.seurat)), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="Cell Cycle\nS-G2M", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[7]] = ggplot(emb[meta[order(meta$percent.rb),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$percent.rb)), size=2, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="percent.rb")

grid.arrange(grobs=my.plots, ncol=2)


dim.orig.ident <- ggplot(emb, aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=meta$orig.ident[sample(x = seq(nrow(emb)), size = nrow(emb), replace = FALSE)]), size=0.8, alpha = 0.6, pch = 19) + 
    scale_colour_manual(values = rainbow(length(table(my.int@meta.data$orig.ident))) ) +
    theme_classic() + labs(colour="Dataset", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

dim.orig.ident

DV domain plots

To identify the different DV domains of the neuron and progenitor clusters, we plot their specific markers.

plots_neur <- lapply(neurons, feat_list_plot)
Not all features are present in your object! Removing:  LHX2 LHX9 BARHL1 BARHL2 
Not all features are present in your object! Removing:  DRGX 
Not all features are present in your object! Removing:  LBX1 
Not all features are present in your object! Removing:  LBX1 DRGX 
Not all features are present in your object! Removing:  LBX1 
Not all features are present in your object! Removing:  EVX1 
Not all features are present in your object! Removing:  LHX3 
Not all features are present in your object! Removing:  MNX1 LHX3 ISL2 

DE analysis

Here we do the differential expression analysis, and end up with the marker genes lists. We can also see the marker gene dot plot, for the top 2 marker genes per cluster

# Find all the marker genes, with these thresholds MAST
semarkers = FindAllMarkers(my.int,
                           features = my.int[[\integrated\]]@var.features, 
                           only.pos = TRUE, 
                           min.pct = 0.25, 
                           logfc.threshold =  0.5,
                           latent.vars = c(\CC.Difference.seurat\), 
                           test.use = \MAST\, 
                           assay = \RNA\, 
                           return.thresh = 0.05)

# We only keep the significant ones
semarkers <- semarkers %>%
  filter(p_val_adj < 0.05) %>% 
  rename(Gene.stable.ID = gene) %>% 
  left_join(gnames, by = \Gene.stable.ID\)


# Take only the top 10
semrk10 = semarkers %>% group_by(cluster) %>% top_n(-10, p_val_adj)
semrk1 = semarkers %>% group_by(cluster) %>% top_n(-1, p_val_adj)

modplots::mDotPlot2(my.int, 
          features = unique(semrk1$Gene.stable.ID), 
          cols = c(\grey\, \black\),  
          gnames = gnames, dot.scale = 6) +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))

DoHeatmap(my.int, semrk1$Gene.stable.ID)

save

saveRDS(my.int, paste0(\~/spinal_cord_paper/data/\, my.int@project.name, \_seurat_\,format(Sys.Date(), \%d%m%y\),\.rds\))

write.table(semarkers, sep = \\t\, row.names = T, col.names = T,
            file = paste0(\~/spinal_cord_paper/data/\, my.int@project.name, \_fullDE_\,format(Sys.Date(), \%d%m%y\),\.txt\), quote = F)

write.table(semrk10, sep = \\t\, row.names = T, col.names = T,
            file = paste0(\~/spinal_cord_paper/data/\, my.int@project.name, \_top10DE_\,format(Sys.Date(), \%d%m%y\),\.txt\), quote = F)
# Date and time of Rendering
Sys.time()
[1] \2023-02-07 11:10:07 CET\
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /scicore/soft/apps/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib/libopenblas_sandybridgep-r0.3.1.so

locale:
[1] en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggdendro_0.1.22    cowplot_1.1.1      patchwork_1.1.1    gridExtra_2.3     
 [5] ggplot2_3.3.3      tidyr_1.1.3        RColorBrewer_1.1-2 Rtsne_0.15        
 [9] dplyr_1.0.10       SeuratObject_4.0.2 Seurat_4.0.5      

loaded via a namespace (and not attached):
  [1] fastmatch_1.1-0             plyr_1.8.6                 
  [3] igraph_1.2.6                lazyeval_0.2.2             
  [5] sp_1.4-5                    splines_4.1.0              
  [7] listenv_0.8.0               scattermore_0.7            
  [9] GenomeInfoDb_1.28.0         digest_0.6.27              
 [11] htmltools_0.5.1.1           ips_0.0.11                 
 [13] fansi_0.5.0                 magrittr_2.0.1             
 [15] memoise_2.0.0               tensor_1.5                 
 [17] cluster_2.1.2               ROCR_1.0-11                
 [19] globals_0.16.2              Biostrings_2.60.0          
 [21] matrixStats_0.58.0          modplots_1.0.0             
 [23] spatstat.sparse_3.0-0       prettyunits_1.1.1          
 [25] colorspace_2.0-1            blob_1.2.1                 
 [27] ggrepel_0.9.1               xfun_0.34                  
 [29] crayon_1.4.1                RCurl_1.98-1.3             
 [31] jsonlite_1.7.2              spatstat.data_3.0-0        
 [33] phangorn_2.7.0              ape_5.5                    
 [35] survival_3.2-11             zoo_1.8-9                  
 [37] glue_1.6.2                  polyclip_1.10-0            
 [39] gtable_0.3.0                zlibbioc_1.38.0            
 [41] XVector_0.32.0              leiden_0.3.9               
 [43] DelayedArray_0.18.0         SingleCellExperiment_1.14.1
 [45] future.apply_1.7.0          BiocGenerics_0.38.0        
 [47] abind_1.4-5                 scales_1.1.1               
 [49] pheatmap_1.0.12             DBI_1.1.1                  
 [51] miniUI_0.1.1.1              Rcpp_1.0.7                 
 [53] progress_1.2.2              viridisLite_0.4.0          
 [55] xtable_1.8-4                reticulate_1.22            
 [57] spatstat.core_2.1-2         bit_4.0.4                  
 [59] stats4_4.1.0                htmlwidgets_1.5.3          
 [61] httr_1.4.2                  ellipsis_0.3.2             
 [63] ica_1.0-2                   XML_3.99-0.6               
 [65] farver_2.1.0                pkgconfig_2.0.3            
 [67] sass_0.4.0                  uwot_0.1.10                
 [69] deldir_1.0-6                utf8_1.2.1                 
 [71] labeling_0.4.2              tidyselect_1.2.0           
 [73] rlang_1.0.6                 reshape2_1.4.4             
 [75] later_1.2.0                 AnnotationDbi_1.54.0       
 [77] munsell_0.5.0               tools_4.1.0                
 [79] cachem_1.0.5                cli_3.4.1                  
 [81] generics_0.1.3              RSQLite_2.2.7              
 [83] ggridges_0.5.3              org.Gg.eg.db_3.13.0        
 [85] evaluate_0.20               stringr_1.4.0              
 [87] fastmap_1.1.0               yaml_2.2.1                 
 [89] goftest_1.2-2               knitr_1.41                 
 [91] bit64_4.0.5                 fitdistrplus_1.1-6         
 [93] purrr_0.3.4                 RANN_2.6.1                 
 [95] KEGGREST_1.32.0             pbapply_1.4-3              
 [97] future_1.30.0               nlme_3.1-152               
 [99] mime_0.10                   compiler_4.1.0             
[101] plotly_4.10.0               png_0.1-7                  
[103] spatstat.utils_3.0-1        tibble_3.1.8               
[105] bslib_0.2.5.1               stringi_1.6.2              
[107] highr_0.9                   lattice_0.20-44            
[109] Matrix_1.3-3                vctrs_0.5.1                
[111] pillar_1.8.1                lifecycle_1.0.3            
[113] spatstat.geom_3.0-3         lmtest_0.9-38              
[115] jquerylib_0.1.4             RcppAnnoy_0.0.19           
[117] data.table_1.14.0           bitops_1.0-7               
[119] irlba_2.3.3                 GenomicRanges_1.44.0       
[121] httpuv_1.6.1                R6_2.5.0                   
[123] promises_1.2.0.1            KernSmooth_2.23-20         
[125] IRanges_2.26.0              parallelly_1.33.0          
[127] codetools_0.2-18            MASS_7.3-54                
[129] assertthat_0.2.1            MAST_1.18.0                
[131] SummarizedExperiment_1.22.0 withr_2.4.2                
[133] sctransform_0.3.3           S4Vectors_0.30.0           
[135] GenomeInfoDbData_1.2.6      hms_1.1.0                  
[137] mgcv_1.8-35                 parallel_4.1.0             
[139] quadprog_1.5-8              grid_4.1.0                 
[141] rpart_4.1-15                rmarkdown_2.17             
[143] MatrixGenerics_1.4.0        Biobase_2.52.0             
[145] shiny_1.6.0                
---
title: "Seurat workflow of the integrated Gg lumb 1 and 2 data"
author: "Fabio Sacher"
date: "06.02.2023"
output:
  html_document:
    toc: TRUE
    toc_float: TRUE
    df_print: paged
  html_notebook:
    fig_height: 7
    fig_width: 8
editor_options:
  chunk_output_type: inline
---

```{r, setup, include=FALSE}
knitr::opts_chunk$set(
  comment = '', fig.width = 10, fig.height = 7
)
```

Render this script with > sbatch ~/spinal_cord_paper/scripts/Seurat_Gg_NT_int_array.sh

# load the data

the following workflow is based on:
 - [https://github.com/satijalab/seurat/issues/1500] Cell cycle regression
 - [https://github.com/satijalab/seurat/issues/1836] General workflow
 - [https://github.com/satijalab/seurat/issues/2590] Integrate all features (although used in the integration script)

```{r libraries, warning = FALSE, message = FALSE, echo = T, results = 'hide'}
library(Seurat)
library(dplyr)
library(Rtsne)
library(RColorBrewer)
library(tidyr)
library(ggplot2)
library(gridExtra)
library(patchwork)
library(cowplot)
library(ggdendro)

```

```{r input, echo = T, results = 'hide', message=FALSE, warning=FALSE}

gnames <- modplots::gnames
# load the integrated seurat
my.int <- readRDS(file = "~/spinal_cord_paper/data/Gg_lumb_integrated_250723.rds")

my.int@project.name <- "Gg_lumb_int"

my.int
```

Date: `r format(Sys.Date(), "%d.%m.%y")`

# inspect

We order the plot by nCount_RNA to prevent overplotting of the last sample (default order is the group.by ident).

```{r inspection}
# have a look at the PC and the previously calculated UMAP
PCAPlot(
  my.int,
  group.by = "orig.ident",
  order = "nCount_RNA"
  )

DimPlot(
  my.int,
  reduction = "umap",
  group.by = "orig.ident",
  order = "nCount_RNA"
  )

```

# cell cycle scoring

Now we can score the cell cycle stage, using Seurats function. For this wee need the ortholog of the distributed cell stage marker lists. 

We do the CC.difference calculation at this stage - and not prior to integration - based on the suggestion from: [https://github.com/satijalab/seurat/issues/1500]

We add the scores of stages S and G2M, as well as the difference between them to the metadata with the names: S, G2M, CC.Difference

```{r , message=FALSE, warning=FALSE, echo = T, results = 'hide'}
# Load the orhtology table
ortho_gg_mm_v102 <- readRDS("~/spinal_cord_paper/data/ortho_gg_mm_v102.rds") 

colnames(ortho_gg_mm_v102) <- c(
  "GG_gene_ID",
  "GG_gene_Name",
  "MM_gene_ID",
  "MM_gene_Name",
  "ortho_conf",
  "homolog_type"
)

# A list of cell cycle markers, from Tirosh et al, 2015, is loaded with Seurat.  We can
# segregate this list into markers of G2/M phase and markers of S phase
s.genes <- ortho_gg_mm_v102 %>%
  dplyr::mutate(MM_gene_Name = toupper(MM_gene_Name)) %>%
  dplyr::filter(MM_gene_Name %in% cc.genes$s.genes) %>%
  dplyr::arrange(match(MM_gene_Name, cc.genes$s.genes)) %>%
  dplyr::pull(GG_gene_ID)

g2m.genes <- ortho_gg_mm_v102 %>%
  dplyr::mutate(MM_gene_Name = toupper(MM_gene_Name)) %>%
  dplyr::filter(MM_gene_Name %in% cc.genes$g2m.genes) %>%
  dplyr::arrange(match(MM_gene_Name, cc.genes$g2m.genes)) %>%
  dplyr::pull(GG_gene_ID) 

t0 <- Sys.time()
my.int <- CellCycleScoring(
  my.int,
  s.features = s.genes,
  g2m.features = g2m.genes,
  set.ident = TRUE
  )
paste0("Seurats CC scoring took ", Sys.time() - t0, " seconds to run.")

my.int$CC.Difference.seurat <- my.int$S.Score - my.int$G2M.Score
# view cell cycle scores and phase assignments
head(my.int[[]])

rm(t0, s.genes, g2m.genes)
```

## PCA plot of non-regressed data
```{r}
PCAPlot(my.int, group.by = "Phase")
```


# rescale integrated assay

We rescale the data to regress out the CC.difference

```{r scale.data-regress.cc.diff}
all_genes <- rownames(my.int)

my.int <- ScaleData(
  my.int,
  features = all_genes,
  vars.to.regress = "CC.Difference.seurat"
)
```

# PCA

```{r}
# Run the actual PCA (by default uses var.features of assay)
my.int <- RunPCA(my.int, verbose = F)

PCAPlot(my.int, group.by = "Phase")

# Which dimensions will we choose?
hist(my.int@reductions$pca@stdev^2, breaks = 500)

my.dimensions=1:20

```

# Dim Reduction

We will run the tSNE. Using the FFT-accelerated Interpolation-based t-SNE (FIt-SNE).
We run two, a normal tSNE, and an exaggerated tSNE, where clusters are tighter togheter. This is located under the xtsne name.

```{r tsne, message=FALSE, warning=FALSE, echo = T, results = 'hide'}

# Get the tSNE function
source("~/Software/FIt-SNE-master/fast_tsne.R")

my.tsne = fftRtsne(my.int@reductions$pca@cell.embeddings[,my.dimensions],
                   max_iter = 1500,
                   learning_rate =  round(dim(my.int)[2]/12),
                   initialization =(my.int@reductions$pca@cell.embeddings[,1:2]/my.int@reductions$pca@stdev[1])*0.0001,
                   perplexity_list = c(25, round(dim(my.int)[2]/100)),
                   fast_tsne_path="~/Software/FIt-SNE-master/bin/fast_tsne")

colnames(my.tsne) = c("tsne_1", "tsne_2")
rownames(my.tsne) = colnames(my.int)

my.int[["tsne"]] = CreateDimReducObject(embeddings = my.tsne, key = "tsne_", assay = DefaultAssay(my.int), global = T)

```

# Clustering

Here we perform the Louvain-jaccard clustering implemented in Seurat.
We can see the tree of clusters, to see how the clusters relate in the PCA space.   
We also use the tree, to check if any of the terminal pairs of sisters should be merged. This is determined based on a minimum of 20 DEs between the clusters.

```{r clusters, message=FALSE, warning=FALSE, echo = T, results = 'hide'}

# Find first the nearest neighbors
my.int <- FindNeighbors(object = my.int, dims=my.dimensions, verbose = F)

# Then the actual clusters
my.int <- FindClusters(object = my.int, resolution = 1, verbose = F, random.seed = 42)

# Check the tree of clusters, to see what's the relationship between them
my.int <- BuildClusterTree(my.int, dims = my.dimensions, verbose = F)
plot(Tool(object = my.int, slot = 'BuildClusterTree'))

# We are gonna check for DEs using the non integrated data. We are only gonna test genes that have variability, so we calculate variable genes
my.int <- FindVariableFeatures(my.int, assay = "RNA")


# Only the genes with variability > median
my.HVF <- HVFInfo(my.int, assay = "RNA")
my.HVF <- rownames(my.HVF)[which(my.HVF[,3] > (median(my.HVF[,3])))]
# We check for pairs of clusters, how mayn DEs they have. If less than n, we merge them
keep.check <- T
while (keep.check == T) {
  
  keep.check <- F
  # Check the tree of clusters, to see what's the relationship between them
  my.int <- BuildClusterTree(my.int, dims = my.dimensions, verbose = F)
  # Check only the terminal sisters
  to.check = ips::terminalSisters(my.int@tools$BuildClusterTree)
  for (i in to.check) {
    # DE between the sisters
    my.DE <- FindMarkers(my.int, i[1], i[2], test.use = "MAST", latent.vars = c("CC.Difference.seurat"),
                         min.pct = 0.25, verbose = T, assay = "RNA", features = my.HVF,) %>%
      dplyr::filter(abs(avg_log2FC) > 0.5) %>%
      dplyr::filter(p_val_adj < 0.05)
    
    # If less than 5, merge, and repeat
    if (dim(my.DE)[1] < 5) {
      cat(paste0(dim(my.DE)[1], " genes differentially expressed between clusters ",i[1]," and ",i[2]," merging \n"))
      my.int <- SetIdent(my.int, cells = WhichCells(my.int, idents = i[2]), value = i[1])
      keep.check <- T
    }
    print(i)
  }
}
rm(to.check, my.HVF, my.DE)

```

```{r tsne_again, fig.height = 12, fig.width = 12}

# renumber starting from 1
my.ID <- factor(
  Idents(my.int),
  levels= levels(Idents(my.int))[base::order(as.numeric(levels(Idents(my.int))))])
levels(my.ID) <- seq(length(levels(my.ID)))
Idents(my.int) <- my.ID
my.int[["seurat_clusters"]] <- my.ID

# Check again the clusters
dim1 <- DimPlot(my.int, reduction = "tsne", cols = rainbow(length(levels(my.ID))), label = T, label.size = 5, pt.size = 1)
dim1
```

Plot the tree again

```{r renumbered tree}
# tree based on PCA dims
my.int <- BuildClusterTree(my.int, dims = my.dimensions, verbose = F)
plot(Tool(object = my.int, slot = 'BuildClusterTree'))
```

Now that we have the final reductions, we'll choose one and we look at the statistics of the cells. 

```{r}
modplots::mFeaturePlot(my.int, my.features = c("OLIG2", "SOX9", "TUBB3", "SHH", "SLC18A3", "GATA2", "PAX2", "TLX3", "IGFBP7", "HBBA", "IFI30", "MSX2", "PLP1"), gnames = gnames)
```

```{r qplots, fig.height = 15, fig.width = 10, message=FALSE, warning=FALSE, echo = T}

# set and get dim.reduct embeddings
my.reduc <- "tsne"
emb <- data.frame(Embeddings(my.int, my.reduc))
colnames(emb) <- c("reduc_1", "reduc_2")

meta <- my.int[[]] %>%
  tibble::rownames_to_column("cell_ID")


my.plots = list()

my.plots[[1]] = ggplot(emb[meta[order(meta$nCount_RNA),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$nCount_RNA)), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="UMI count", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[2]] = ggplot(emb[meta[order(meta$nFeature_RNA),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$nFeature_RNA)), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="gene count", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[3]] = ggplot(emb[meta[order(meta$nCount_SCT),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$nCount_RNA)), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="UMI count (SCT)", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[4]] = ggplot(emb[meta[order(meta$nFeature_SCT),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$nFeature_RNA)), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="gene count (SCT)", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[5]] = ggplot(emb[meta[order(meta$percent.mt),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=(sort(meta$percent.mt))), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="log1p MT percent", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[6]] = ggplot(emb[meta[order(meta$CC.Difference.seurat),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$CC.Difference.seurat)), size=1, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="Cell Cycle\nS-G2M", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

my.plots[[7]] = ggplot(emb[meta[order(meta$percent.rb),]$cell_ID, ], aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=sort(meta$percent.rb)), size=2, alpha = 0.4, pch = 19) + 
    scale_colour_gradientn(colours = c("gray90","gray90","gray80","yellow", "orange", "red", "darkred", "darkred")) +
    theme_classic() + labs(colour="percent.rb")

grid.arrange(grobs=my.plots, ncol=2)

```


```{r orig.ident-red.plot, fig.height = 10, fig.width = 15}

dim.orig.ident <- ggplot(emb, aes(x = reduc_1, y = reduc_2)) +
    geom_point(aes(color=meta$orig.ident[sample(x = seq(nrow(emb)), size = nrow(emb), replace = FALSE)]), size=0.8, alpha = 0.6, pch = 19) + 
    scale_colour_manual(values = rainbow(length(table(my.int@meta.data$orig.ident))) ) +
    theme_classic() + labs(colour="Dataset", x = paste0(my.reduc, "_1"), y = paste0(my.reduc, "_2"))

dim.orig.ident
```

# DV domain plots

To identify the different DV domains of the neuron and progenitor clusters, we plot their specific markers.

```{r DV-dom}
# POU4F1 in there twice because other genes are not expressed and the code breaks
neurons <- list(dI1 = c("LHX2","LHX9","BARHL1","BARHL2","POU4F1","POU4F1"),
  dI2 = c("LHX1","LHX5","POU4F1"),
  dI3 = c("ISL1","TLX3","DRGX","POU4F1"),
  dI4 = c("LBX1","PAX2","LHX1","LHX5"),
  dI5 = c("LBX1","LMX1B","TLX3","DRGX","POU4F1"),
  dI6 = c("LBX1","PAX2","LHX1","LHX5"),
  V0 = c("EVX1","PAX2","LHX1","LHX5"),
  V1 = c("EN1","PAX2","LHX1","LHX5"),
  V2a = c("VSX1","SOX14","LHX3"),
  V2b = c("GATA2","GATA3","TAL1"),
  MN =  c("MNX1","ISL1","LHX3","ISL2", "SLC18A3"))

prog <- list(dp1_3 =  c("PAX6","IRX3","IRX5","MSX1","PAX3","PAX7"),
  dp4 = c("PAX6","IRX3","IRX5","GSX1","PAX3","PAX7"),
  dp5 = c("PAX6","IRX3","IRX5","DBX2","GSX1","PAX3","PAX7"),
  dp6 = c("PAX6","IRX3","IRX5","DBX2","LEUTX","PAX3","PAX7"),
  p0 = c("PAX6","IRX3","IRX5","DBX2","LEUTX"),
  p1 = c("PAX6","IRX3","IRX5","DBX2","PRDM12"),
  p2 = c("PAX6","IRX3","IRX5","FOXN4","NKX6-1"),
  pMN = c("PAX6","OLIG2","NKX6-1"),
  p3 = c("NKX2-8","NKX2-2","NKX6-1"))

# allows to use mFeaturePlot with lapply
feat_list_plot <- function(x) {
 plot <- modplots::mFeaturePlot(my.int, my.features = x,
                       gnames = gnames, size = 0.2, return = TRUE)
 return(plot)
}

tsne_dim <- TSNEPlot(
  my.int,
  reduction = "tsne",
  cols = rainbow(length(levels(my.ID))),
  pt.size = 0.01,
  label.size = 1,
  label = TRUE
) +
  ggplot2::theme(legend.position = "none")

plots_prog <- lapply(prog, feat_list_plot)
plots_neur <- lapply(neurons, feat_list_plot)


pdf(paste0("~/spinal_cord_paper/annotations/figures/DV_prog_domain_",my.int@project.name ,".pdf"), width = 7, height = 5)
  for (j in names(prog)) {
    plots_prog[[j]][["tsne"]] <- tsne_dim
    gridExtra::grid.arrange(grobs = plots_prog[[j]], ncol = 3, top = j)
  }
dev.off()

pdf(paste0("~/spinal_cord_paper/annotations/figures/DV_neur_domain_",my.int@project.name ,".pdf"), width = 7, height = 5)
  for (j in names(neurons)) {
    plots_neur[[j]][["tsne"]] <- tsne_dim
    gridExtra::grid.arrange(grobs = plots_neur[[j]], ncol = 3, top = j)
  }
  dev.off()
```

# DE analysis

Here we do the differential expression analysis, and end up with the marker genes lists.
We can also see the marker gene dot plot, for the top 2 marker genes per cluster

```{r DE, fig.height=10, message=FALSE, warning=FALSE, echo = T}

# Find all the marker genes, with these thresholds MAST
semarkers = FindAllMarkers(my.int,
                           features = my.int[["integrated"]]@var.features, 
                           only.pos = TRUE, 
                           min.pct = 0.25, 
                           logfc.threshold =  0.5,
                           latent.vars = c("CC.Difference.seurat"), 
                           test.use = "MAST", 
                           assay = "RNA", 
                           return.thresh = 0.05)

# We only keep the significant ones
semarkers <- semarkers %>%
  filter(p_val_adj < 0.05) %>% 
  rename(Gene.stable.ID = gene) %>% 
  left_join(gnames, by = "Gene.stable.ID")


# Take only the top 10
semrk10 = semarkers %>% group_by(cluster) %>% top_n(-10, p_val_adj)
semrk1 = semarkers %>% group_by(cluster) %>% top_n(-1, p_val_adj)

modplots::mDotPlot2(my.int, 
          features = unique(semrk1$Gene.stable.ID), 
          cols = c("grey", "black"),  
          gnames = gnames, dot.scale = 6) +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))

DoHeatmap(my.int, semrk1$Gene.stable.ID)
```

# save

```{r saving, message=FALSE, warning=FALSE, echo = T}

saveRDS(my.int, paste0("~/spinal_cord_paper/data/", my.int@project.name, "_seurat_",format(Sys.Date(), "%d%m%y"),".rds"))

write.table(semarkers, sep = "\t", row.names = T, col.names = T,
            file = paste0("~/spinal_cord_paper/data/", my.int@project.name, "_fullDE_",format(Sys.Date(), "%d%m%y"),".txt"), quote = F)

write.table(semrk10, sep = "\t", row.names = T, col.names = T,
            file = paste0("~/spinal_cord_paper/data/", my.int@project.name, "_top10DE_",format(Sys.Date(), "%d%m%y"),".txt"), quote = F)

```

```{r sessionInfo}
# Date and time of Rendering
Sys.time()

sessionInfo()
```
